Learning Sampling-Based 6D Object Pose Estimation

The task of 6D object pose estimation, i.e. of estimating an object position (three degrees of freedom) and orientation (three degrees of freedom) from images is an essential building block of many modern applications, such as robotic grasping, autonomous driving, or augmented reality. Automatic pose estimation systems have to overcome a variety of visual ambiguities, including texture-less objects, clutter, and occlusion. Since many applications demand real time performance the efficient use of computational resources is an additional challenge. In this thesis, we will take a probabilistic stance on trying to overcome said issues. We build on a highly successful automatic pose estimation framework based on predicting pixel-wise correspondences between the camera coordinate system and the local coordinate system of the object. These dense correspondences are used to generate a pool of hypotheses, which in turn serve as a starting point in a final search procedure. We will present three systems that each use probabilistic modeling and sampling to improve upon different aspects of the framework. The goal of the first system, System I, is to enable pose tracking, i.e. estimating the pose of an object in a sequence of frames instead of a single image. By including information from previous frames tracking systems can resolve many visual ambiguities and reduce computation time. System I is a particle filter (PF) approach. The PF represents its belief about the pose in each frame by propagating a set of samples through time. Our system uses the process of hypothesis generation from the original framework as part of a proposal distribution that efficiently concentrates samples in the appropriate areas. In System II, we focus on the problem of evaluating the quality of pose hypotheses. This task plays an essential role in the final search procedure of the original framework. We use a convolutional neural network (CNN) to assess the quality of an hypothesis by comparing rendered and observed images. To train the CNN we view it as part of an energy-based probability distribution in pose space. This probabilistic perspective allows us to train the system under the maximum likelihood paradigm. We use a sampling approach to approximate the required gradients. The resulting system for pose estimation yields superior results in particular for highly occluded objects. In System III, we take the idea of machine learning a step further. Instead of learning to predict an hypothesis quality measure, to be used in a search procedure, we present a way of learning the search procedure itself. We train a reinforcement learning (RL) agent, termed PoseAgent, to steer the search process and make optimal use of a given computational budget. PoseAgent dynamically decides which hypothesis should be refined next, and which one should ultimately be output as final estimate. Since the search procedure includes discrete non-differentiable choices, training of the system via gradient descent is not easily possible. To solve the problem, we model behavior of PoseAgent as non-deterministic stochastic policy, which is ultimately governed by a CNN. This allows us to use a sampling-based stochastic policy gradient training procedure. We believe that some of the ideas developed in this thesis, such as the sampling-driven probabilistically motivated training of a CNN for the comparison of images or the search procedure implemented by PoseAgent have the potential to be applied in fields beyond pose estimation as well

PoseAgent: Budget-Constrained 6D Object Pose Estimation via Reinforcement Learning

State-of-the-art computer vision algorithms often achieve efficiency by making discrete choices about which hypotheses to explore next. This allows allocation of computational resources to promising candidates, however, such decisions are non-differentiable. As a result, these algorithms are hard to train in an end-to-end fashion. In this work we propose to learn an efficient algorithm for the task of 6D object pose estimation. Our system optimizes the parameters of an existing state-of-the art pose estimation system using reinforcement learning, where the pose estimation system now becomes the stochastic policy, parametrized by a CNN. Additionally, we present an efficient training algorithm that dramatically reduces computation time. We show empirically that our learned pose estimation procedure makes better use of limited resources and improves upon the state-of-the-art on a challenging dataset. Our approach enables differentiable end-to-end training of complex algorithmic pipelines and learns to make optimal use of a given computational budget

Learning Analysis-by-Synthesis for 6D Pose Estimation in RGB-D Images

Analysis-by-synthesis has been a successful approach for many tasks in computer vision, such as 6D pose estimation of an object in an RGB-D image which is the topic of this work. The idea is to compare the observation with the output of a forward process, such as a rendered image of the object of interest in a particular pose. Due to occlusion or complicated sensor noise, it can be difficult to perform this comparison in a meaningful way. We propose an approach that "learns to compare", while taking these difficulties into account. This is done by describing the posterior density of a particular object pose with a convolutional neural network (CNN) that compares an observed and rendered image. The network is trained with the maximum likelihood paradigm. We observe empirically that the CNN does not specialize to the geometry or appearance of specific objects, and it can be used with objects of vastly different shapes and appearances, and in different backgrounds. Compared to state-of-the-art, we demonstrate a significant improvement on two different datasets which include a total of eleven objects, cluttered background, and heavy occlusion.Comment: 16 pages, 8 figure

Fully Unsupervised Probabilistic Noise2Void

Image denoising is the first step in many biomedical image analysis pipelines and Deep Learning (DL) based methods are currently best performing. A new category of DL methods such as Noise2Void or Noise2Self can be used fully unsupervised, requiring nothing but the noisy data. However, this comes at the price of reduced reconstruction quality. The recently proposed Probabilistic Noise2Void (PN2V) improves results, but requires an additional noise model for which calibration data needs to be acquired. Here, we present improvements to PN2V that (i) replace histogram based noise models by parametric noise models, and (ii) show how suitable noise models can be created even in the absence of calibration data. This is a major step since it actually renders PN2V fully unsupervised. We demonstrate that all proposed improvements are not only academic but indeed relevant.Comment: Accepted at ISBI 202

{\mu}Split: efficient image decomposition for microscopy data

We present {\mu}Split, a dedicated approach for trained image decomposition in the context of fluorescence microscopy images. We find that best results using regular deep architectures are achieved when large image patches are used during training, making memory consumption the limiting factor to further improving performance. We therefore introduce lateral contextualization (LC), a memory efficient way to train powerful networks and show that LC leads to consistent and significant improvements on the task at hand. We integrate LC with U-Nets, Hierarchical AEs, and Hierarchical VAEs, for which we formulate a modified ELBO loss. Additionally, LC enables training deeper hierarchical models than otherwise possible and, interestingly, helps to reduce tiling artefacts that are inherently impossible to avoid when using tiled VAE predictions. We apply {\mu}Split to five decomposition tasks, one on a synthetic dataset, four others derived from real microscopy data. LC achieves SOTA results (average improvements to the best baseline of 2.36 dB PSNR), while simultaneously requiring considerably less GPU memory.Comment: Published at ICCV 2023. 10 pages, 7 figures, 9 pages supplement, 8 supplementary figure

DenoiSeg: Joint Denoising and Segmentation

Microscopy image analysis often requires the segmentation of objects, but training data for this task is typically scarce and hard to obtain. Here we propose DenoiSeg, a new method that can be trained end-to-end on only a few annotated ground truth segmentations. We achieve this by extending Noise2Void, a self-supervised denoising scheme that can be trained on noisy images alone, to also predict dense 3-class segmentations. The reason for the success of our method is that segmentation can profit from denoising, especially when performed jointly within the same network. The network becomes a denoising expert by seeing all available raw data, while co-learning to segment, even if only a few segmentation labels are available. This hypothesis is additionally fueled by our observation that the best segmentation results on high quality (very low noise) raw data are obtained when moderate amounts of synthetic noise are added. This renders the denoising-task non-trivial and unleashes the desired co-learning effect. We believe that DenoiSeg offers a viable way to circumvent the tremendous hunger for high quality training data and effectively enables few-shot learning of dense segmentations.Comment: 10 pages, 4 figures, 2 pages supplement (4 figures

Leveraging Self-supervised Denoising for Image Segmentation

Deep learning (DL) has arguably emerged as the method of choice for the detection and segmentation of biological structures in microscopy images. However, DL typically needs copious amounts of annotated training data that is for biomedical projects typically not available and excessively expensive to generate. Additionally, tasks become harder in the presence of noise, requiring even more high-quality training data. Hence, we propose to use denoising networks to improve the performance of other DL-based image segmentation methods. More specifically, we present ideas on how state-of-the-art self-supervised CARE networks can improve cell/nuclei segmentation in microscopy data. Using two state-of-the-art baseline methods, U-Net and StarDist, we show that our ideas consistently improve the quality of resulting segmentations, especially when only limited training data for noisy micrographs are available.Comment: accepted at ISBI 202

A divide and conquer strategy for the maximum likelihood localization of low intensity objects

In cell biology and other fields the automatic accurate localization of sub-resolution objects in images is an important tool. The signal is often corrupted by multiple forms of noise, including excess noise resulting from the amplification by an electron multiplying charge-coupled device (EMCCD). Here we present our novel Nested Maximum Likelihood Algorithm (NMLA), which solves the problem of localizing multiple overlapping emitters in a setting affected by excess noise, by repeatedly solving the task of independent localization for single emitters in an excess noise-free system. NMLA dramatically improves scalability and robustness, when compared to a general purpose optimization technique. Our method was successfully applied for in vivo localization of fluorescent proteins

Imaging in focus: An introduction to denoising bioimages in the era of deep learning

Fluorescence microscopy enables the direct observation of previously hidden dynamic processes of life, allowing profound insights into mechanisms of health and disease. However, imaging of live samples is fundamentally limited by the toxicity of the illuminating light and images are often acquired using low light conditions. As a consequence, images can become very noisy which severely complicates their interpretation. In recent years, deep learning (DL) has emerged as a very successful approach to remove this noise while retaining the useful signal. Unlike classical algorithms which use well-defined mathematical functions to remove noise, DL methods learn to denoise from example data, providing a powerful content-aware approach. In this review, we first describe the different types of noise that typically corrupt fluorescence microscopy images and introduce the denoising task. We then present the main DL-based denoising methods and their relative advantages and disadvantages. We aim to provide insights into how DL-based denoising methods operate and help users choose the most appropriate tools for their applications